Scientific research relies on computer software, yet software is not always developed following practices that ensure its quality and sustainability. This manuscript does not aim to propose new software development best practices, but rather to provide simple recommendations that encourage the adoption of existing best practices. Software development best practices promote better quality software, and better quality software improves the reproducibility and reusability of research. These recommendations are designed around Open Source values, and provide practical suggestions that contribute to making research software and its source code more discoverable, reusable and transparent. This manuscript is aimed at developers, but also at organisations, projects, journals and funders that can increase the quality and sustainability of research software by encouraging the adoption of these recommendations.

Australian Genome Research Facility Ltd Melbourne Australia

Australian National Data Service Melbourne Australia

Barcelona Supercomputing Center Barcelona 08034 Spain

BBMRI at Alpen Adria University Klagenfurt Klagenfurt Austria

BBMRI ERIC Neue Stiftingtalstraße 2 B 6 Graz 8010 Austria

Center for Open Science Charlottesville VA USA

Central European Institute of Technology Brno Czech Republic

Centre for Language and Speech Technology Radboud University Nijmegen Nijmegen Netherlands

Computational Biology Division Department of Integrative Biomedical Sciences Institute for Infectious Disease and Molecular Medicine University of Cape Town Cape Town South Africa

CSL Limited Bio21 Institute 30 Flemington Road Parkville Victoria 3010 Australia

Department of Biochemistry and Molecular Biomedicine Universitat de Barcelona Barcelona 08028 Spain

Department of Computer Science University of Illinois Urbana Champaign Urbana IL USA

Department of Electrical and Computer Engineering University of Illinois Urbana Champaign Urbana IL USA

DETI IEETA University of Aveiro Aveiro Portugal

Dutch TechCenter for Life Sciences and ELIXIR NL Utrecht Netherlands

ELIXIR CZ Faculty of Information Technology Czech Technical University Prague Prague Czech Republic

ELIXIR DE and de NBI Bioinformatics Group Department of Computer Science University of Freiburg Freiburg Germany

ELIXIR DK Technical University of Denmark Denmark Denmark

ELIXIR EE Institute of Computer Science University of Tartu Tartu Estonia

ELIXIR ES Spanish National Bioinformatics Institute Calle de Melchor Fernández Almagro 3 Madrid 28029 Spain

ELIXIR Hub Wellcome Genome Campus Hinxton CB10 1SD UK

ELIXIR SE National Bioinformatics Infrastructure Sweden Stockholm University Stockholm Sweden

ELIXIR SI Faculty of Medicine University of Ljubljana Ljubljana Slovenia

ELIXIR UK Software Sustainability Institute School of Computer Science University of Manchester Oxford Road Manchester M13 9PL UK

EMBL Australia Bioinformatics Resource Lab 14 The University of Melbourne 700 Swanston St Parkville Victoria 3053 Australia

EMBL EBI Wellcome Genome Campus Hinxton CB10 1SD UK

Faculty of Information Technology Monash University Victoria Australia

GRIB Institut Hospital del Mar d'Investigacions Mèdiques Universitat Pompeu Fabra Barcelona Spain

IBPM CNR Department of Biochemical Sciences Sapienza University of Rome Rome Italy

National Center for Supercomputing Applications University of Illinois at Urbana Champaign Urbana IL USA

National Centre for Biomolecular Research Masaryk University Brno Czech Republic

National eResearch Collaboration Tools and Resources Victoria 3010 Australia

Netherlands eScience Center Science Park 140 Amsterdam 1098 XG Netherlands

Oxford e Research Centre University of Oxford Oxford UK

Repositive Ltd Future Business Centre Cambridge UK

School of Agriculture Food and Wine University of Adelaide Adelaide Australia

School of Information Sciences University of Illinois Urbana Champaign Urbana IL USA

Science and Technologies Facilities Council Swindon UK

Software Sustainability Institute JCMB University of Edinburgh Edinburgh EH9 3FD UK

Software Sustainability Institute Web and Internet Science University of Southampton Southampton UK

Stemformatics University of Melbourne Melbourne Australia

Zobrazit více v PubMed

Artaza H, Chue Hong N, Manuel C, et al. : Top 10 metrics for life science software good practices [version 1; referees: 2 approved]. F1000Res. 2016;5: pii: ELIXIR-2000. 10.12688/f1000research.9206.1 PubMed DOI PMC

Brase J: Datacite - A Global Registration Agency for Research Data. SSRN Electronic Journal.n.d. 10.2139/ssrn.1639998 DOI

Corpas M, Jimenez R, Carbon SJ, et al. : BioJS: an open source standard for biological visualisation – its status in 2014 [version 1; referees: 2 approved]. F1000Res. 2014;3:55. 10.12688/f1000research.3-55.v1 PubMed DOI PMC

Crouch S, Chue Hong N, Hettrick S, et al. : The Software Sustainability Institute: Changing Research Software Attitudes and Practices. Computing in Science & Engineering. 2013;15(6):74–80. 10.1109/MCSE.2013.133 DOI

DagstuhlEAS: DagstuhlEAS/draft-Manifesto. GitHub. 2017. Accessed January 5. Reference Source

Eijssen L, Evelo C, Kok R, et al. : The Dutch Techcentre for Life Sciences: Enabling data-intensive life science research in the Netherlands [version 2; referees: 2 approved, 1 approved with reservations]. F1000Res. 2016;4:33. 10.12688/f1000research.6009.2 PubMed DOI PMC

Fogel K: Producing Open Source Software: How to Run a Successful Free Software Project.O’Reilly Media, Inc.2005. Reference Source

Gilb T: Principles of Software Engineering Management.Addison-Wesley Professional,1988. Reference Source

Goble C: Better Software, Better Research. IEEE Internet Computing. 2014;18(5):4–8. 10.1109/MIC.2014.88 DOI

Gómez J, García LJ, Salazar GA, et al. : BioJS: An Open Source JavaScript Framework for Biological Data Visualization. Bioinformatics. 2013;29(8):1103–4. 10.1093/bioinformatics/btt100 PubMed DOI PMC

Hannay JE, MacLeod C, Singer J, et al. : How Do Scientists Develop and Use Scientific Software?In 2009 ICSE Workshop on Software Engineering for Computational Science and Engineering2009. 10.1109/secse.2009.5069155 DOI

Henry VJ, Bandrowski AE, Pepin AS, et al. : OMICtools: An Informative Directory for Multi-Omic Data Analysis. Database (Oxford). 2014;2014: pii: bau069. 10.1093/database/bau069 PubMed DOI PMC

Hettrick S, Antonioletti M, Carr L, et al. : UK Research Software Survey 2014.Accessed November 27.2016. 10.5281/zenodo.14809 DOI

Ince DC, Hatton L, Graham-Cumming J: The Case for Open Computer Programs. Nature. 2012;482(7386):485–88. 10.1038/nature10836 PubMed DOI

Ison J, Rapacki K, Ménager H, et al. : Tools and Data Services Registry: A Community Effort to Document Bioinformatics Resources. Nucleic Acids Res. 2016;44(D1):D38–47. 10.1093/nar/gkv1116 PubMed DOI PMC

Leprevost Fda V, Barbosar VC, Francisco EL, et al. : On best practices in the development of bioinformatics software. Front Genet. 2014;5:199. 10.3389/fgene.2014.00199 PubMed DOI PMC

List M, Ebert P, Albrecht F: Ten Simple Rules for Developing Usable Software in Computational Biology. PLoS Comput Biol. 2017;13(1):e1005265. 10.1371/journal.pcbi.1005265 PubMed DOI PMC

McKiernan EC, Bourne PE, Brown CT, et al. : How open science helps researchers succeed. eLife. 2016;5: pii: e16800. 10.7554/elife.16800 PubMed DOI PMC

Mulgan G, Steinberg T, Salem O: Wide Open: Open Source Methods and Their Future Potential.Demos Medical Publishing.2005. Reference Source

Nosek BA, Alter G, Banks GC, et al. : SCIENTIFIC STANDARDS. Promoting an open research culture. Science. American Association for the Advancement of Science,2015;348(6242):1422–25. 10.1126/science.aab2374 PubMed DOI PMC

Perez-Riverol Y, Gatto L, Wang R, et al. : Ten Simple Rules for Taking Advantage of Git and GitHub. PLoS Comput Biol. 2016;12(7):e1004947. 10.1371/journal.pcbi.1004947 PubMed DOI PMC

Perez-Riverol Y, Wang R, Hermjakob H, et al. : Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective. Biochim Biophys Acta. 2014;1844(1 Pt A):63–76. 10.1016/j.bbapap.2013.02.032 PubMed DOI PMC

Popp KM: Best Practices for Commercial Use of Open Source Software: Business Models, Processes and Tools for Managing Open Source Software. BoD – Books on Demand. 2015. Reference Source

Prlić A, Procter JB: Ten simple rules for the open development of scientific software. PLoS Comput Biol. 2012;8(12):e1002802. 10.1371/journal.pcbi.1002802 PubMed DOI PMC

Smith AM, Katz DS, Niemeyer KE, et al. : Software Citation Principles. PeerJ Comput Sci. 2016;2:e86 10.7717/peerj-cs.86 DOI

Wilkinson MD, Dumontier M, Aalbersberg IJ, et al. : The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. 2016;3:160018. 10.1038/sdata.2016.18 PubMed DOI PMC

Wilson G, Aruliah DA, Brown CT, et al. : Best practices for scientific computing. PLoS Biol. 2014;12(1):e1001745. 10.1371/journal.pbio.1001745 PubMed DOI PMC

Wilson G, Bryan J, Cranston K, et al. : Good Enough Practices in Scientific Computing.2016. Reference Source PubMed PMC

Wilson G: Software Carpentry: lessons learned [version 1; referees: 3 approved]. F1000Res. 2014;3:62. 10.12688/f1000research.3-62.v1 PubMed DOI PMC

HTSinfer: inferring metadata from bulk Illumina RNA-Seq libraries

A research data management (RDM) community for ELIXIR